Category Jekyll
There are lots of powerful things you can do with the Markdown editor. If you’ve gotten pretty comfortable with writing in Markdown, then you may enjoy some more advanced tips...
Even the press, the classroom, the platform, and the pulpit in many instances do not give us objective and unbiased truths. To save man from the morass of propaganda, in...
Education must also train one for quick, resolute and effective thinking. To think incisively and to think for one’s self is very difficult.
This website collects some notes, tutorials and handsout used for
microbial bioinformatics training events.
Two popular formats to store structured data are XML and JSON.
They are used everywhere in computer science and appear more and more often in
bioinformatics analyses as well.
Here we introduce the FASTA format, to store DNA and protein sequences.
Here we introduce the SAM format, to store the result of a mapping
of one or more DNA sequences against a reference genome
Here we introduce some of the most used bioinformatics formats.
Two popular formats to store structured data are XML and JSON.
They are used everywhere in computer science and appear more and more often in
bioinformatics analyses as well.
Category bash
The Integrative Genome Browser (IGV) from the
Broad Institute can be considered the microscope for the
Bioinformatician.
How to use SSH to connect to a remote server
Pipes: how to combine commands to perform complex tasks
Redirection: how to save to a file the output from shell commands
Here we introduce some new commands and concepts to work with the command line, in particular
for text file parsing and manipulation.
A tutorial on the Linux command line (CLI) and its use in bioinformatics.
A very first primer on the Linux command line for bioinformatics. Open your terminal and start typing the first commands! There are several pages dedicated to Bash in this website,...
The problem and its solution
The problem and its solution
A basic introduction on passing parameters to shell scripts
We can instruct our scripts to stop when a problem is found with the set -euo pipefail directive.
The idea to check if some condition is true before executing some commands is very simple and useful. The Bash syntax, for historical reasons, is probably the ugliest you’ll ever...
After a small introduction to Bash scripting, we finally create a first bioinformatics script… introducing one of the loops we can use with the shell. A loop is a structure...
After using the Linux terminal for a while, everyone wants to be able to write simple “scripts” to perform repetitive tasks. They looks like recipes, with the main difference of...
Category tutorial
A walk through based on a lecture by Antrea Pavlou at the 11th EBAME workshop
The Integrative Genome Browser (IGV) from the
Broad Institute can be considered the microscope for the
Bioinformatician.
How to use SSH to connect to a remote server
Pipes: how to combine commands to perform complex tasks
Redirection: how to save to a file the output from shell commands
Here we introduce some new commands and concepts to work with the command line, in particular
for text file parsing and manipulation.
A tutorial on the Linux command line (CLI) and its use in bioinformatics.
A very first primer on the Linux command line for bioinformatics. Open your terminal and start typing the first commands! There are several pages dedicated to Bash in this website,...
MetaPhage is a complete reads-to-report pipeline for viral metagenomics. It is a Nextflow pipeline that can be run on a local machine or on a cluster. It is designed to...
vConTACT2 is a tool to infer the taxonomic relationship of viral sequences with
a network-based approach, based on whole genome gene-sharing profiles.
To identify putative viral sequences without using a classifier, we can use a de novo assembly approach. We first need to perform a standard metagenome assembly, then we need to...
Phanta profiling requires these steps:
A short overview of tools used and how to get them
The goal of this section is to get a set of reads to test our programs with
This “virome primer” is designed to provide a short overview on viromics and the tools available to analyse viral metagenomes. The tutorial is agnostic to the environment, and can be...
“Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or...
First, let’s run the pipeline!
CLIMB Workshop on Metagenomics taxonomic profiling
CLIMB Workshop on Metabarcoding (16S) analysis
On our first day we well cover the concepts behind taxonomic classification using Kraken2 (and Bracken), and see how to remove host reads and perform the quality checks (and filtering)....
Kaiju can be installed, as usual, from Conda.
Like Kraken2, we have access to pre-built databases, and for this
tutorial we used the nr 2021-02-24 (52 GB).
When performing multiple operations on the same dataset, as some of you pointed out during the workshop, we often want to collate metadata. R is the ideal choice for doing...
To determine the microbial composition in your samples, one method to get this information is taxonomic read profiling. Here you compare your reads to a database of interest. Kraken2 is...
A more complex script to perform a
for loop
is available from GitHub as shown below:
To determine the microbial composition in your samples, one method to get this information is taxonomic read profiling. Here you compare your reads to a database of interest. Kraken2 is...
In our workshop we provided a Kraken2 database for you to use. However, most of the time, you would need to create a database for your own host. For the...
Our goal here is to create a small and artificial set of sequences to be classified using Kraken2,
to practice with its parameters and its output formats.
First steps Log in into the server You should find a directory called sequences in your home. List the files in that directory (for example with ls -l ~/sequences) The...
If you are working with host-associate microbiome, we are usually only interested in the microbial fraction and not the host DNA. In fact, host DNA can intefere with the read...
An introduction to the “Tidyverse”
Today we will use Braken to recalibrate our estimations, and a set of scripts to merge multiple samples in a single table, and see how to filter it. We will...
On our first day we well cover the concepts behind taxonomic classification using Kraken2 (and Bracken), and see how to remove host reads and perform the quality checks (and filtering)....
From the Command line to R
Yesterday we introduced the whole workflow to analyze 16S reads, and the powerful framework that Qiime2
introduced that:
Deblur is an alternative method to produce
a set of denoised sequences. While DADA2 can
natively support paired-end reads, Deblur can
only manage single-end reads.
The problem and its solution
The problem and its solution
A basic introduction on passing parameters to shell scripts
We can instruct our scripts to stop when a problem is found with the set -euo pipefail directive.
The idea to check if some condition is true before executing some commands is very simple and useful. The Bash syntax, for historical reasons, is probably the ugliest you’ll ever...
After a small introduction to Bash scripting, we finally create a first bioinformatics script… introducing one of the loops we can use with the shell. A loop is a structure...
After using the Linux terminal for a while, everyone wants to be able to write simple “scripts” to perform repetitive tasks. They looks like recipes, with the main difference of...
Category singularity
A basic introduction to Singularity containers
CLIMB Workshop on Metabarcoding (16S) analysis
From the Command line to R
Yesterday we introduced the whole workflow to analyze 16S reads, and the powerful framework that Qiime2
introduced that:
Deblur is an alternative method to produce
a set of denoised sequences. While DADA2 can
natively support paired-end reads, Deblur can
only manage single-end reads.
Category 16S
From the Command line to R
Yesterday we introduced the whole workflow to analyze 16S reads, and the powerful framework that Qiime2
introduced that:
Deblur is an alternative method to produce
a set of denoised sequences. While DADA2 can
natively support paired-end reads, Deblur can
only manage single-end reads.
A walk through based on a lecture by Antrea Pavlou at the 11th EBAME workshop
If you’ve ever sequenced a clinical or environmental microbial sample,
you’ve almost certainly encountered the problem of host contamination.
CLIMB Workshop on Metagenomics taxonomic profiling
On our first day we well cover the concepts behind taxonomic classification using Kraken2 (and Bracken), and see how to remove host reads and perform the quality checks (and filtering)....
Kaiju can be installed, as usual, from Conda.
Like Kraken2, we have access to pre-built databases, and for this
tutorial we used the nr 2021-02-24 (52 GB).
When performing multiple operations on the same dataset, as some of you pointed out during the workshop, we often want to collate metadata. R is the ideal choice for doing...
To determine the microbial composition in your samples, one method to get this information is taxonomic read profiling. Here you compare your reads to a database of interest. Kraken2 is...
A more complex script to perform a
for loop
is available from GitHub as shown below:
To determine the microbial composition in your samples, one method to get this information is taxonomic read profiling. Here you compare your reads to a database of interest. Kraken2 is...
In our workshop we provided a Kraken2 database for you to use. However, most of the time, you would need to create a database for your own host. For the...
Our goal here is to create a small and artificial set of sequences to be classified using Kraken2,
to practice with its parameters and its output formats.
First steps Log in into the server You should find a directory called sequences in your home. List the files in that directory (for example with ls -l ~/sequences) The...
If you are working with host-associate microbiome, we are usually only interested in the microbial fraction and not the host DNA. In fact, host DNA can intefere with the read...
An introduction to the “Tidyverse”
Today we will use Braken to recalibrate our estimations, and a set of scripts to merge multiple samples in a single table, and see how to filter it. We will...
On our first day we well cover the concepts behind taxonomic classification using Kraken2 (and Bracken), and see how to remove host reads and perform the quality checks (and filtering)....
Category nextflow
First, let’s run the pipeline!
Category docker
Category conda
Category virome
MetaPhage is a complete reads-to-report pipeline for viral metagenomics. It is a Nextflow pipeline that can be run on a local machine or on a cluster. It is designed to...
vConTACT2 is a tool to infer the taxonomic relationship of viral sequences with
a network-based approach, based on whole genome gene-sharing profiles.
To identify putative viral sequences without using a classifier, we can use a de novo assembly approach. We first need to perform a standard metagenome assembly, then we need to...
Phanta profiling requires these steps:
A short overview of tools used and how to get them
The goal of this section is to get a set of reads to test our programs with
This “virome primer” is designed to provide a short overview on viromics and the tools available to analyse viral metagenomes. The tutorial is agnostic to the environment, and can be...
“Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or...
Category ebame
This “virome primer” is designed to provide a short overview on viromics and the tools available to analyse viral metagenomes. The tutorial is agnostic to the environment, and can be...
vConTACT2 is a tool to infer the taxonomic relationship of viral sequences with
a network-based approach, based on whole genome gene-sharing profiles.
To identify putative viral sequences without using a classifier, we can use a de novo assembly approach. We first need to perform a standard metagenome assembly, then we need to...
Phanta profiling requires these steps:
A short overview of tools used and how to get them
MetaPhage is a complete reads-to-report pipeline for viral metagenomics. It is a Nextflow pipeline that can be run on a local machine or on a cluster. It is designed to...
Category python
More data structures in Python using standard libraries.
Built-in data structures in Python: lists, tuples, sets, and dictionaries.
Counting the number of occurrences of each word in a text is a common task in computational linguistics. It is also a good example of how to use Python to...
Some YouTube videos and tutorials to learn how to use the command line.
Category distribution
Counting the number of occurrences of each word in a text is a common task in computational linguistics. It is also a good example of how to use Python to...
Some YouTube videos and tutorials to learn how to use the command line.
Category project
Counting the number of occurrences of each word in a text is a common task in computational linguistics. It is also a good example of how to use Python to...
Some YouTube videos and tutorials to learn how to use the command line.
Category climb
This walkthrough can be completely performed on any Linux terminal where Miniconda/Mamba have been installed, including a web based terminal offered by CLIMB BIG DATA new notebooks.
The MRC CLIMB BIG DATA
project offers modern storage in the form of
S3 buckets,
an object storage introduced by Amazon Web Services (AWS).
Category data-structures
More data structures in Python using standard libraries.
Built-in data structures in Python: lists, tuples, sets, and dictionaries.
Category perl
Perl has been the scripting language enabling the first bioinformatics radiation,
for example “saving” the human genome project.
Category post
Logan and Logan Search: making the world’s sequencing data searchable
Category protein-language-models
A walk through based on a lecture by Antrea Pavlou at the 11th EBAME workshop
